Repeated blocks in the TaALMT1 promoter as well as a transposon insertion in the TaMATE1B upstream region have been correlated with the level of gene expression, organic acid efflux, and ultimately aluminum (Al3+) resistance in wheat (Triticum aestivum L.). In this study, we investigated the allelic polymorphism related to the TaALMT1 and TaMATE1B promoter regions in 300 Brazilian wheat genotypes and the correlation of that variation with root growth on acid soil. In addition, SSR markers were used to determine the genetic variability of the genotypes. Seven TaALMT1 promoter alleles (Types I–VII) were detected based on size of PCR products. The most common alleles were Type V and Type VI (71.3 and 11.9 %, respectively), and these are generally associated with higher levels of TaALMT1 expression and Al3+ resistance. The promoter alleles Type I and Type II, which are usually associated with Al3+ sensitivity, were detected in 12.2 % of the genotypes. The insertion in the TaMATE1B promoter, associated with greater Al3+ resistance, was identified in 80 genotypes. Combination among the alleles allowed the separation in 12 haplotypes were 68 genotypes presented the TaALMT1 promoters Type V and Type VI along with the transposon insertion in the TaMATE1B promoter. However, the most represented haplotype was Type V without the insertion (176 genotypes). Short-term soil experiment, performed in 33 genotypes representing the 12 haplotypes, revealed that the higher relative root length was observed in some genotypes presenting TaALMT1 promoters Type V or Type VI and the transposon insertion in the TaMATE1B promoter. Moreover, when comparing genotypes inside the same haplotype, the transposon insertion was significantly advantageous for a few materials. However, the majority the genotypes presenting the insertion in the TaMATE1B promoter did not outperform the genotypes without the insertion but showing the same TaALMT1 promoter. Analysis using SSR markers, with an average PIC of 0.60, showed high genetic diversity among the genotypes belonging to different haplotypes. The alleles and the genetically diverse genotypes reported here should be considered for wheat-breeding programs aiming increments in wheat Al3+ resistance.